Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

text edits to standardize reference formats #295

Merged
merged 1 commit into from
Feb 2, 2024
Merged

text edits to standardize reference formats #295

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
18 changes: 9 additions & 9 deletions R/fit.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -295,7 +295,7 @@ NULL
#'
#' *Reference for local trends:*
#'
#' Barnett, L.A.K., E.J. Ward, S.C. Anderson. Improving estimates of species
#' Barnett, L.A.K., E.J. Ward, S.C. Anderson. 2021. Improving estimates of species
#' distribution change by incorporating local trends. Ecography. 44(3):427-439.
#' \doi{10.1111/ecog.05176}.
#'
Expand All @@ -311,14 +311,14 @@ NULL
#' *Discussion of and illustration of some decision points when fitting these
#' models:*
#'
#' Commander, C.J.C., Barnett, L.A.K., Ward, E.J., Anderson, S.C., and
#' Essington, T.E. 2022. The shadow model: how and why small choices in
#' Commander, C.J.C., L.A.K. Barnett, E.J. Ward, S.C. Anderson, T.E.
#' Essington. 2022. The shadow model: how and why small choices in
#' spatially explicit species distribution models affect predictions. PeerJ 10:
#' e12783. \doi{10.7717/peerj.12783}.
#'
#' *Application and description of threshold/break-point models:*
#'
#' Essington, T.E. S.C. Anderson, L.A.K. Barnett, H.M. Berger, S.A. Siedlecki,
#' Essington, T.E., S.C. Anderson, L.A.K. Barnett, H.M. Berger, S.A. Siedlecki,
#' E.J. Ward. 2022. Advancing statistical models to reveal the effect of
#' dissolved oxygen on the spatial distribution of marine taxa using thresholds
#' and a physiologically based index. Ecography. 2022: e06249
Expand All @@ -333,7 +333,7 @@ NULL
#' *Several sections of the original TMB model code were adapted from the
#' VAST R package:*
#'
#' Thorson, J.T., 2019. Guidance for decisions using the Vector Autoregressive
#' Thorson, J.T. 2019. Guidance for decisions using the Vector Autoregressive
#' Spatio-Temporal (VAST) package in stock, ecosystem, habitat and climate
#' assessments. Fish. Res. 210:143–161.
#' \doi{10.1016/j.fishres.2018.10.013}.
Expand All @@ -343,16 +343,16 @@ NULL
#' idea behind the TMB prediction approach were adapted from the glmmTMB R
#' package:*
#'
#' Mollie E. Brooks, Kasper Kristensen, Koen J. van Benthem, Arni Magnusson,
#' Casper W. Berg, Anders Nielsen, Hans J. Skaug, Martin Maechler and Benjamin
#' M. Bolker (2017). glmmTMB Balances Speed and Flexibility Among Packages for
#' Brooks, M.E., K. Kristensen, K.J. van Benthem, A. Magnusson,
#' C.W. Berg, A. Nielsen, H.J. Skaug, M. Maechler, B.M. Bolker.
#' 2017. glmmTMB Balances Speed and Flexibility Among Packages for
#' Zero-inflated Generalized Linear Mixed Modeling. The R Journal, 9(2):378-400.
#' \doi{10.32614/rj-2017-066}.
#'
#' *Implementation of geometric anisotropy with the SPDE and use of random
#' field GLMMs for index standardization*:
#'
#' Thorson, J.T., Shelton, A.O., Ward, E.J., and Skaug, H.J. 2015.
#' Thorson, J.T., A.O. Shelton, E.J. Ward, H.J. Skaug. 2015.
#' Geostatistical delta-generalized linear mixed models improve precision for
#' estimated abundance indices for West Coast groundfishes. ICES J. Mar. Sci.
#' 72(5): 1297–1310. \doi{10.1093/icesjms/fsu243}.
Expand Down
Loading